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Deng J, Yang JC, Feng Y, Xu ZJ, Kuča K, Liu M, Sun LH. AP-1 and SP1 trans-activate the expression of hepatic CYP1A1 and CYP2A6 in the bioactivation of AFB 1 in chicken. Sci China Life Sci 2024:10.1007/s11427-023-2512-6. [PMID: 38703348 DOI: 10.1007/s11427-023-2512-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/09/2024] [Indexed: 05/06/2024]
Abstract
Dietary exposure to aflatoxin B1 (AFB1) is harmful to the health and performance of domestic animals. The hepatic cytochrome P450s (CYPs), CYP1A1 and CYP2A6, are the primary enzymes responsible for the bioactivation of AFB1 to the highly toxic exo-AFB1-8,9-epoxide (AFBO) in chicks. However, the transcriptional regulation mechanism of these CYP genes in the liver of chicks in AFB1 metabolism remains unknown. Dual-luciferase reporter assay, bioinformatics and site-directed mutation results indicated that specificity protein 1 (SP1) and activator protein-1 (AP-1) motifs were located in the core region -1,063/-948, -606/-541 of the CYP1A1 promoter as well as -636/-595, -503/-462, -147/-1 of the CYP2A6 promoter. Furthermore, overexpression and decoy oligodeoxynucleotide technologies demonstrated that SP1 and AP-1 were pivotal transcriptional activators regulating the promoter activity of CYP1A1 and CYP2A6. Moreover, bioactivation of AFB1 to AFBO could be increased by upregulation of CYP1A1 and CYP2A6 expression, which was trans-activated owing to the upregulalion of AP-1, rather than SP1, stimulated by AFB1-induced reactive oxygen species. Additionally, nano-selenium could reduce ROS, downregulate AP-1 expression and then decrease the expression of CYP1A1 and CYP2A6, thus alleviating the toxicity of AFB1. In conclusion, AP-1 and SP1 played important roles in the transactivation of CYP1A1 and CYP2A6 expression and further bioactivated AFB1 to AFBO in chicken liver, which could provide novel targets for the remediation of aflatoxicosis in chicks.
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Affiliation(s)
- Jiang Deng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia-Cheng Yang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yue Feng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ze-Jing Xu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kamil Kuča
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 50003, Czech Republic
| | - Meng Liu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lv-Hui Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Wang X, Li L, Guo L, Feng Y, Du Z, Jiang W, Wu X, Zheng J, Xiao X, Zheng H, Sun Y, Ma H. Robust miniature Cas-based transcriptional modulation by engineering Un1Cas12f1 and tethering Sso7d. Mol Ther 2024; 32:910-919. [PMID: 38351611 DOI: 10.1016/j.ymthe.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/16/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
The miniature V-F CRISPR-Cas12f system has been repurposed for gene editing and transcription modulation. The small size of Cas12f satisfies the packaging capacity of adeno-associated virus (AAV) for gene therapy. However, the efficiency of Cas12f-mediated transcriptional activation varies among different target sites. Here, we developed a robust miniature Cas-based transcriptional activation or silencing system using Un1Cas12f1. We engineered Un1Cas12f1 and the cognate guide RNA and generated miniCRa, which led to a 1,319-fold increase in the activation of the ASCL1 gene. The activity can be further increased by tethering DNA-binding protein Sso7d to miniCRa and generating SminiCRa, which reached a 5,628-fold activation of the ASCL1 gene and at least hundreds-fold activation at other genes examined. We adopted these mutations of Un1Cas12f1 for transcriptional repression and generated miniCRi or SminiCRi, which led to the repression of ∼80% on average of eight genes. We generated an all-in-one AAV vector AIOminiCRi used to silence the disease-related gene SERPINA1. AIOminiCRi AAVs led to the 70% repression of the SERPINA1 gene in the Huh-7 cells. In summary, miniCRa, SminiCRa, miniCRi, and SminiCRi are robust miniature transcriptional modulators with high specificity that expand the toolbox for biomedical research and therapeutic applications.
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Affiliation(s)
- Xiangnan Wang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lingyun Li
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Li Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ying Feng
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | | | - Wei Jiang
- Belief Biomed (Shanghai), Shanghai, China
| | - Xia Wu
- School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jing Zheng
- Belief Biomed (Shanghai), Shanghai, China
| | - Xiao Xiao
- Belief Biomed (Shanghai), Shanghai, China
| | - Hui Zheng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yadong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hanhui Ma
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Zhang Z, Huo J, Velo J, Zhou H, Flaherty A, Saier MH. Comprehensive Characterization of fucAO Operon Activation in Escherichia coli. Int J Mol Sci 2024; 25:3946. [PMID: 38612757 PMCID: PMC11011485 DOI: 10.3390/ijms25073946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Wildtype Escherichia coli cells cannot grow on L-1,2-propanediol, as the fucAO operon within the fucose (fuc) regulon is thought to be silent in the absence of L-fucose. Little information is available concerning the transcriptional regulation of this operon. Here, we first confirm that fucAO operon expression is highly inducible by fucose and is primarily attributable to the upstream operon promoter, while the fucO promoter within the 3'-end of fucA is weak and uninducible. Using 5'RACE, we identify the actual transcriptional start site (TSS) of the main fucAO operon promoter, refuting the originally proposed TSS. Several lines of evidence are provided showing that the fucAO locus is within a transcriptionally repressed region on the chromosome. Operon activation is dependent on FucR and Crp but not SrsR. Two Crp-cAMP binding sites previously found in the regulatory region are validated, where the upstream site plays a more critical role than the downstream site in operon activation. Furthermore, two FucR binding sites are identified, where the downstream site near the first Crp site is more important than the upstream site. Operon transcription relies on Crp-cAMP to a greater degree than on FucR. Our data strongly suggest that FucR mainly functions to facilitate the binding of Crp to its upstream site, which in turn activates the fucAO promoter by efficiently recruiting RNA polymerase.
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Affiliation(s)
- Zhongge Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.H.); (J.V.); (A.F.)
| | | | | | | | | | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.H.); (J.V.); (A.F.)
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Ramsey KM, Barrick D. Unraveling paralog-specific Notch signaling through thermodynamics of ternary complex formation and transcriptional activation of chimeric receptors. Protein Sci 2024; 33:e4947. [PMID: 38511488 PMCID: PMC10962485 DOI: 10.1002/pro.4947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 03/22/2024]
Abstract
Notch signaling in humans is mediated by four paralogous receptors that share conserved architectures and possess overlapping, yet non-redundant functions. The receptors share a canonical activation pathway wherein upon extracellular ligand binding, the Notch intracellular domain (NICD) is cleaved from the membrane and translocates to the nucleus where its N-terminal RBP-j-associated molecule (RAM) region and ankyrin repeat (ANK) domain bind transcription factor CSL and recruit co-activator Mastermind-like-1 (MAML1) to activate transcription. However, different paralogs can lead to distinct outcomes. To better understand paralog-specific differences in Notch signaling, we performed a thermodynamic analysis of the Notch transcriptional activation complexes for all four Notch paralogs using isothermal titration calorimetry. Using chimeric constructs, we find that the RAM region is the primary determinant of stability of binary RAMANK:CSL complexes, and that the ANK regions are largely the determinants of MAML1 binding to pre-formed RAMANK:CSL complexes. Free energies of these binding reactions (ΔGRA and ΔGMAML) vary among the four Notch paralogs, although variations for Notch2, 3, and 4 offset in the free energy of the ternary complex (ΔGTC, where ΔGTC = ΔGRA + ΔGMAML). To probe how these affinity differences affect Notch signaling, we performed transcriptional activation assays with the paralogous and chimeric NICDs, and analyzed the results with an independent multiplicative model that quantifies contributions of the paralogous RAM, ANK, and C-terminal regions (CTR) to activation. This analysis shows that transcription activation correlates with ΔGTC, but that activation is further modified by CTR identity in a paralog-specific way.
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Affiliation(s)
- Kristen M. Ramsey
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Doug Barrick
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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Zheng F, Kawabe Y, Kamihira M. RNA Aptamer-Mediated Gene Activation Systems for Inducible Transgene Expression in Animal Cells. ACS Synth Biol 2024; 13:230-241. [PMID: 38073086 DOI: 10.1021/acssynbio.3c00472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
RNA expression analyses can be used to obtain various information from inside cells, such as physical conditions, the chemical environment, and endogenous signals. For detecting RNA, the system regulating intracellular gene expression has the potential for monitoring RNA expression levels in real time within living cells. Synthetic biology provides powerful tools for detecting and analyzing RNA inside cells. Here, we devised an RNA aptamer-mediated gene activation system, RAMGA, to induce RNA-triggered gene expression activation by employing an inducible complex formation strategy grounded in synthetic biology. This methodology connects DNA-binding domains and transactivators through target RNA using RNA-binding domains, including phage coat proteins. MS2 bacteriophage coat protein fused with a transcriptional activator and PP7 bacteriophage coat protein fused with the tetracycline repressor (tetR) can be bridged by target RNA encoding MS2 and PP7 stem-loops, resulting in transcriptional activation. We generated recombinant CHO cells containing an inducible GFP expression module governed by a minimal promoter with a tetR-responsive element. Cells carrying the trigger RNA exhibited robust reporter gene expression, whereas cells lacking it exhibited no expression. GFP expression was upregulated over 200-fold compared with that in cells without a target RNA expression vector. Moreover, this system can detect the expression of mRNA tagged with aptamer tags and modulate reporter gene expression based on the target mRNA level without affecting the expression of the original mRNA-encoding gene. The RNA-triggered gene expression systems developed in this study have potential as a new platform for establishing gene circuits, evaluating endogenous gene expression, and developing novel RNA detectors.
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Affiliation(s)
- Feiyang Zheng
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshinori Kawabe
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Zhang Z, Zhang H, Hu B, Luan Y, Zhu K, Ma B, Zhang Z, Zheng X. R-Loop Defines Neural Stem/Progenitor Cells During Mouse Neurodevelopment. Stem Cells Dev 2023; 32:719-730. [PMID: 37823735 DOI: 10.1089/scd.2023.0196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Neural stem/progenitor cells (NSPCs) are present in the mammalian brain throughout life and are involved in neurodevelopment and central nervous system repair. Although typical epigenetic signatures, including DNA methylation, histone modifications, and microRNAs, play a pivotal role in regulation of NSPCs, several of the epigenetic regulatory mechanisms of NSPCs remain unclear. Thus, defining a novel epigenetic feature of NSPCs is crucial for developing stem cell therapy to address neurologic disorders caused by injury. In this study, we aimed to define the R-loop, a three-stranded nucleic acid structure, as an epigenetic characteristic of NSPCs during neurodevelopment. Our results demonstrated that R-loop levels change dynamically throughout neurodevelopment. Cells with high levels of R-loops consistently decreased and were enriched in the area of neurogenesis. Additionally, these cells costained with SOX2 during neurodevelopment. Furthermore, these cells with high R-loop levels expressed Ki-67 and exhibited a high degree of overlap with the transcriptional activation markers, H3K4me3, ser5, and H3K27ac. These findings suggest that R-loops may serve as an epigenetic feature for transcriptional activation in NSPCs, indicating their role in gene expression regulation and neurogenesis.
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Affiliation(s)
- Zhe Zhang
- Department of Stomatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Hanyue Zhang
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Baoqi Hu
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yan Luan
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Kun Zhu
- Department of Neurology, and The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bo Ma
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhichao Zhang
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaoyan Zheng
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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7
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Liu J, Chen Y, Nong B, Luo X, Cui K, Li Z, Zhang P, Tan W, Yang Y, Ma W, Liang P, Songyang Z. CRISPR-assisted transcription activation by phase-separation proteins. Protein Cell 2023; 14:874-887. [PMID: 36905356 PMCID: PMC10691850 DOI: 10.1093/procel/pwad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/11/2023] [Indexed: 03/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms. Current CRISPR-activation (CRISPRa) platforms often require multiple components because of inefficient transcriptional activation. Here, we fused different phase-separation proteins to dCas9-VPR (dCas9-VP64-P65-RTA) and observed robust increases in transcriptional activation efficiency. Notably, human NUP98 (nucleoporin 98) and FUS (fused in sarcoma) IDR domains were best at enhancing dCas9-VPR activity, with dCas9-VPR-FUS IDR (VPRF) outperforming the other CRISPRa systems tested in this study in both activation efficiency and system simplicity. dCas9-VPRF overcomes the target strand bias and widens gRNA designing windows without affecting the off-target effect of dCas9-VPR. These findings demonstrate the feasibility of using phase-separation proteins to assist in the regulation of gene expression and support the broad appeal of the dCas9-VPRF system in basic and clinical applications.
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Affiliation(s)
- Jiaqi Liu
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuxi Chen
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Baoting Nong
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiao Luo
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kaixin Cui
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhan Li
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pengfei Zhang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yue Yang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Puping Liang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
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Martinez-Yamout MA, Nasir I, Shnitkind S, Ellis JP, Berlow RB, Kroon G, Deniz AA, Dyson HJ, Wright PE. Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions. Proc Natl Acad Sci U S A 2023; 120:e2313835120. [PMID: 37971402 PMCID: PMC10666024 DOI: 10.1073/pnas.2313835120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREBTAD) construct. The CREBTAD polypeptide chain is largely extended although some compaction is evident in the KID and Q2 domains. Paramagnetic relaxation enhancement reveals transient long-range contacts both within and between the Q1 and Q2 domains while the intervening KID domain is largely devoid of intramolecular interactions. Phosphorylation results in expansion of the KID domain, presumably making it more accessible for binding the CBP/p300 transcriptional coactivators. Our study reveals the complex nature of the interactions within the intrinsically disordered transactivation domain of CREB and provides molecular-level insights into dynamic and transient interactions mediated by the glutamine-rich domains.
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Affiliation(s)
- Maria A. Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Irem Nasir
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Sergey Shnitkind
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Jamie P. Ellis
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Rebecca B. Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Gerard Kroon
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
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Zhu P, Dou C, Song Z, Bi X, Wu X, Miao Y. ELF1/PRR11/ARP2/3 promoted trophoblast cells proliferation and motility in early pregnancy. Am J Reprod Immunol 2023; 90:e13758. [PMID: 37641376 DOI: 10.1111/aji.13758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/02/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND/OBJECTIVE Early pregnancy loss (EPL) is a common adverse pregnancy outcome with an incidence of approximately 10-30%. There are many factors that cause EPL, among which the lack of proliferation and invasive properties of trophoblast cells can lead to embryonic development. Therefore, in this study, the molecular biology of trophoblast cells was investigated. METHODS Placental villous tissues from EPL patients were collected to explore ELF1 and PRR11 gene expression. The proliferation and migration of trophoblast cells were assessed by MTT, crystalline violet staining, and traswell assays, respectively. Western blotting and RT-qPCR were performed to investigate the relationship between ELF1, PRR11, and ARP2/3. F-actin polymerization and FAK activation were evaluated by immunofluorescence and western blotting. Ultimately, ELF1/PRR11/ARP2/3 expression was verified in the EPL mice model RESULTS: ELF1 and PRR11 were lowly expressed in placental villous tissues from EPL. The overexpression of ELF1 and PRR11 promoted proliferation and migration of trophoblast cells. Moreover, while ELF1 bound to the PRR11 promoter and promoted transcriptional activation. Finally, ELF1/PRR11/ARP2/3 showed low expression in the placental tissue of EPL mice. CONCLUSION Our study suggested that PRR11 promoted the motility of trophoblast cells by binding to the ARP2/3 complex to promote F-actin polymerization and FAK activation. In addition, ELF1 bound to the initiation site of PRR11 to promote its transcription. ELF1/PRR11/ARP2/3 may play an important role in EPL.
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Affiliation(s)
- Pengfei Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, Hubei, China
- Center for Reproductive Medicine, Children's Hospital of Shanxi and Women Health Center, Taiyuan, Shanxi, China
| | - Chengli Dou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhijiao Song
- Department of Health Care, Children's Hospital of Shanxi and Women Health Center, Taiyuan, Shanxi, China
| | - Xingyu Bi
- Center for Reproductive Medicine, Children's Hospital of Shanxi and Women Health Center, Taiyuan, Shanxi, China
| | - Xueqing Wu
- Center for Reproductive Medicine, Children's Hospital of Shanxi and Women Health Center, Taiyuan, Shanxi, China
| | - Yiliang Miao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, Hubei, China
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10
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Guerrero M, Ruiz C, Romero A, Robeson L, Ruiz D, Salinas F. The N-Terminal Region of the BcWCL1 Photoreceptor Is Necessary for Self-Dimerization and Transcriptional Activation upon Light Stimulation in Yeast. Int J Mol Sci 2023; 24:11874. [PMID: 37569251 PMCID: PMC10418492 DOI: 10.3390/ijms241511874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
The BcWCL1 protein is a blue-light photoreceptor from the fungus Botrytis cinerea. This protein has a central role in B. cinerea circadian regulation and is an ortholog to WC-1 from Neurospora crassa. The BcWCL1 and WC-1 proteins have similar protein domains, including a LOV (Light Oxygen Voltage) domain for light sensing, two PAS (Per Arnt Sim) domains for protein-protein interaction, and a DNA binding domain from the GATA family. Recently, the blue-light response of BcWCL1 was demonstrated in a version without PAS domains (BcWCL1PAS∆). Here, we demonstrated that BcWCL1PAS∆ is capable of self-dimerization through its N-terminal region upon blue-light stimulation. Interestingly, we observed that BcWCL1PAS∆ enables transcriptional activation as a single component in yeast. By using chimeric transcription factors and the luciferase reporter gene, we assessed the transcriptional activity of different fragments of the N-terminal and C-terminal regions of BcWCL1PAS∆, identifying a functional transcriptional activation domain (AD) in the N-terminal region that belongs to the 9aaTAD family. Finally, we determined that the transcriptional activation levels of BcWCL1PAS∆ AD are comparable to those obtained with commonly used ADs in eukaryotic cells (Gal4 and p65). In conclusion, the BcWCL1PAS∆ protein self-dimerized and activated transcription in a blue-light-dependent fashion, opening future applications of this photoreceptor in yeast optogenetics.
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Affiliation(s)
- Matías Guerrero
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile; (M.G.); (C.R.); (A.R.); (L.R.); (D.R.)
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 8330025, Chile
| | - Carlos Ruiz
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile; (M.G.); (C.R.); (A.R.); (L.R.); (D.R.)
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 8330025, Chile
| | - Andrés Romero
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile; (M.G.); (C.R.); (A.R.); (L.R.); (D.R.)
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 8330025, Chile
| | - Luka Robeson
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile; (M.G.); (C.R.); (A.R.); (L.R.); (D.R.)
| | - Diego Ruiz
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile; (M.G.); (C.R.); (A.R.); (L.R.); (D.R.)
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 8330025, Chile
| | - Francisco Salinas
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile; (M.G.); (C.R.); (A.R.); (L.R.); (D.R.)
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 8330025, Chile
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11
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Li J, Qiu JX, Zeng QH, Zhang N, Xu SX, Jin J, Dong ZC, Chen L, Huang W. OsTOC1 plays dual roles in the regulation of plant circadian clock by functioning as a direct transcription activator or repressor. Cell Rep 2023; 42:112765. [PMID: 37421622 DOI: 10.1016/j.celrep.2023.112765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/28/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
Plant clock function relies on precise timing of gene expression through complex regulatory networks consisting of activators and repressors at the core of oscillators. Although TIMING OF CAB EXPRESSION 1 (TOC1) has been recognized as a repressor involved in shaping oscillations and regulating clock-driven processes, its potential to directly activate gene expression remains unclear. In this study, we find that OsTOC1 primarily acts as a transcriptional repressor for core clock components, including OsLHY and OsGI. Here, we show that OsTOC1 possesses the ability to directly activate the expression of circadian target genes. Through binding to the promoters of OsTGAL3a/b, transient activation of OsTOC1 induces the expression of OsTGAL3a/b, indicating its role as an activator contributing to pathogen resistance. Moreover, TOC1 participates in regulating multiple yield-related traits in rice. These findings suggest that TOC1's function as a transcriptional repressor is not inherent, providing flexibility to circadian regulations, particularly in outputs.
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Affiliation(s)
- Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jia-Xin Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Qing-Hua Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Ning Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Shu-Xuan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jian Jin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Zhi-Cheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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12
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Kallam K, Moreno-Giménez E, Mateos-Fernández R, Tansley C, Gianoglio S, Orzaez D, Patron N. Tunable control of insect pheromone biosynthesis in Nicotiana benthamiana. Plant Biotechnol J 2023. [PMID: 37032497 DOI: 10.1111/pbi.14048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Previous work has demonstrated that plants can be used as production platforms for molecules used in health, medicine, and agriculture. Production has been exemplified in both stable transgenic plants and using transient expression strategies. In particular, species of Nicotiana have been engineered to produce a range of useful molecules, including insect sex pheromones, which are valued for species-specific control of agricultural pests. To date, most studies have relied on strong constitutive expression of all pathway genes. However, work in microbes has demonstrated that yields can be improved by controlling and balancing gene expression. Synthetic regulatory elements that provide control over the timing and levels of gene expression are therefore useful for maximizing yields from heterologous biosynthetic pathways. In this study, we demonstrate the use of pathway engineering and synthetic genetic elements for controlling the timing and levels of production of Lepidopteran sex pheromones in Nicotiana benthamiana. We demonstrate that copper can be used as a low-cost molecule for tightly regulated inducible expression. Further, we show how construct architecture influences relative gene expression and, consequently, product yields in multigene constructs. We compare a number of synthetic orthogonal regulatory elements and demonstrate maximal yields from constructs in which expression is mediated by dCas9-based synthetic transcriptional activators. The approaches demonstrated here provide new insights into the heterologous reconstruction of metabolic pathways in plants.
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Affiliation(s)
- Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - Elena Moreno-Giménez
- Institute for Plant Molecular and Cell Biology (IBMCP), UPV-CSIC, Valencia, Spain
| | | | - Connor Tansley
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - Silvia Gianoglio
- Institute for Plant Molecular and Cell Biology (IBMCP), UPV-CSIC, Valencia, Spain
| | - Diego Orzaez
- Institute for Plant Molecular and Cell Biology (IBMCP), UPV-CSIC, Valencia, Spain
| | - Nicola Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
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13
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Yang R, Zhang G, Dong Z, Wang S, Li Y, Lian F, Liu X, Li H, Wei X, Cui H. Homeobox A3 and KDM6A cooperate in transcriptional control of aerobic glycolysis and glioblastoma progression. Neuro Oncol 2023; 25:635-647. [PMID: 36215227 PMCID: PMC10076951 DOI: 10.1093/neuonc/noac231] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Alterations in transcriptional regulators of glycolytic metabolism have been implicated in brain tumor growth, but the underlying molecular mechanisms remain poorly understood. METHODS Knockdown and overexpression cells were used to explore the functional roles of HOXA3 in cell proliferation, tumor formation, and aerobic glycolysis. Chromatin immunoprecipitation, luciferase assays, and western blotting were performed to verify the regulation of HK2 and PKM2 by HOXA3. PLA, Immunoprecipitation, and GST-pull-down assays were used to examine the interaction of HOXA3 and KDM6A. RESULTS We report that transcription factor homeobox A3 (HOXA3), which is aberrantly highly expressed in glioblastoma (GBM) patients and predicts poor prognosis, transcriptionally activates aerobic glycolysis, leading to a significant acceleration in cell proliferation and tumor growth. Mechanically, we identified KDM6A, a lysine-specific demethylase, as an important cooperator of HOXA3 in regulating aerobic glycolysis. HOXA3 activates KDM6A transcription and recruits KDM6A to genomic binding sites of glycolytic genes, targeting glycolytic genes for transcriptional activation by removing the suppressive histone modification H3K27 trimethylation. Further evidence demonstrates that HOXA3 requires KDM6A for transcriptional activation of aerobic glycolysis and brain tumor growth. CONCLUSIONS Our findings provide a novel molecular mechanism linking HOXA3-mediated transactivation and KDM6A-coupled H3K27 demethylation in regulating glucose metabolism and GBM progression.
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Affiliation(s)
- Rui Yang
- Institute of Precision Medicine, Jining Medical University, Jining 272067, China
| | - Guanghui Zhang
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing 400716, China
| | - Zhen Dong
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing 400716, China
| | - Shanshan Wang
- Institute of Precision Medicine, Jining Medical University, Jining 272067, China
| | - Yanping Li
- Institute of Precision Medicine, Jining Medical University, Jining 272067, China
| | - Fuming Lian
- Institute of Precision Medicine, Jining Medical University, Jining 272067, China
| | - Xiaoran Liu
- Institute of Precision Medicine, Jining Medical University, Jining 272067, China
| | - Haibin Li
- Institute of Precision Medicine, Jining Medical University, Jining 272067, China
| | - Xiaonan Wei
- Institute of Precision Medicine, Jining Medical University, Jining 272067, China
| | - Hongjuan Cui
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing 400716, China
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14
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Guo C, Meza-Sosa KF, Valle-Garcia D, Zhao G, Gao K, Yu L, Zhang H, Chen Y, Sun L, Rockowitz S, Wang S, Jiang S, Lieberman J. The SET oncoprotein promotes estrogen-induced transcription by facilitating establishment of active chromatin. Proc Natl Acad Sci U S A 2023; 120:e2206878120. [PMID: 36791099 PMCID: PMC9974495 DOI: 10.1073/pnas.2206878120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 01/10/2023] [Indexed: 02/16/2023] Open
Abstract
SET is a multifunctional histone-binding oncoprotein that regulates transcription by an unclear mechanism. Here we show that SET enhances estrogen-dependent transcription. SET knockdown abrogates transcription of estrogen-responsive genes and their enhancer RNAs. In response to 17β-estradiol (E2), SET binds to the estrogen receptor α (ERα) and is recruited to ERα-bound enhancers and promoters at estrogen response elements (EREs). SET functions as a histone H2 chaperone that dynamically associates with H2A.Z via its acidic C-terminal domain and promotes H2A.Z incorporation, ERα, MLL1, and KDM3A loading and modulates histone methylation at EREs. SET depletion diminishes recruitment of condensin complexes to EREs and impairs E2-dependent enhancer-promoter looping. Thus, SET boosts E2-induced gene expression by establishing an active chromatin structure at ERα-bound enhancers and promoters, which is essential for transcriptional activation.
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Affiliation(s)
- Changying Guo
- College of Life Science and Technology, Xinjiang University, Urumqi830000, China
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Karla F. Meza-Sosa
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - David Valle-Garcia
- Division of Newborn Medicine and Epigenetics Program, Boston Children's Hospital, Boston, MA02115
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Guomeng Zhao
- China Pharmaceutical University, Nanjing211198, China
| | - Kun Gao
- China Pharmaceutical University, Nanjing211198, China
| | - Liting Yu
- China Pharmaceutical University, Nanjing211198, China
| | | | - Yeqing Chen
- Ying Wu College of Computing, New Jersey Institute of Technology, Newark, NJ07102
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, MA02115
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
| | - Shira Rockowitz
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, MA02115
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
| | - Shouyu Wang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing210093, China
| | - Sheng Jiang
- China Pharmaceutical University, Nanjing211198, China
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
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15
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Dong S, Wang W, Liao Z, Fan Y, Wang Q, Zhang L. MYC-activated LINC00607 promotes hepatocellular carcinoma progression by regulating the miR-584-3p/ROCK1 axis. J Gene Med 2023; 25:e3477. [PMID: 36740760 DOI: 10.1002/jgm.3477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/27/2022] [Accepted: 12/20/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND There have been many reports of long non-coding RNAs (lncRNAs) in tumors, and abnormally expressed lncRNA is closely related to hepatocellular carcinoma (HCC). The mechanism of LINC00607 in HCC has not been reported. METHODS We utilized qPCR to evaluate the RNA expression level. The mechanism of MYC binding to the LINC00607 promoter was revealed through chromatin immunoprecipitation assay and dual luciferase reporter assay. The proliferation and invasive ability were evaluated by CCK-8 and transwell assays. The relation between LINC00607 and miR-584-3p was assessed by RNA immunoprecipitation assay and dual luciferase reporter assay. The level of ROCK1 was evaluated by qPCR and western blot. RESULTS In this research, we found that the expression of LINC00607 was higher in HCC tissues when compared with that in the adjacent non-tumor tissues. Meanwhile, MYC was observed to interact with the LINC00607 promoter, leading to the upregulation of LINC00607 in HCC. We further revealed that LINC00607 functioned as a sponge for miR-584-3p. Cell proliferation and migration assays showed that miR-584-3p may inhibit the HCC progression. Moreover, we found that the miR-584-3p inhibitor could reverse the effects of LINC00607 downregulation in HCC through rescue experiments. Through verification, miR-584-3p bound to the 3' UTR of ROCK1 to downregulate its expression. CONCLUSION LINC00607 regulated by MYC can promote the proliferation, migration and invasion of HCC cells through the miR-584-3p/ROCK1 axis.
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Affiliation(s)
- Shuilin Dong
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Wei Wang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Zhibin Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Yawei Fan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Qi Wang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Lei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China.,Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Shanxi Medical University; Shanxi Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Taiyuan, China
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16
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Ouyang X, Wang Z, Wu B, Yang X, Dong B. The Conserved Transcriptional Activation Activity Identified in Dual-Specificity Tyrosine-(Y)-Phosphorylation-Regulated Kinase 1. Biomolecules 2023; 13:biom13020283. [PMID: 36830653 PMCID: PMC9953678 DOI: 10.3390/biom13020283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Dual-specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 (DYRK1) encodes a conserved protein kinase that is indispensable to neuron development. However, whether DYRK1 possesses additional functions apart from kinase function remains poorly understood. In this study, we firstly demonstrated that the C-terminal of ascidian Ciona robusta DYRK1 (CrDYRK1) showed transcriptional activation activity independent of its kinase function. The transcriptional activation activity of CrDYRK1 could be autoinhibited by a repression domain in the N-terminal. More excitingly, both activation and repression domains were retained in HsDYRK1A in humans. The genes, activated by the activation domain of HsDYRK1A, are mainly involved in ion transport and neuroactive ligand-receptor interaction. We further found that numerous mutation sites relevant to the DYRK1A-related intellectual disability syndrome locate in the C-terminal of HsDYRK1A. Then, we identified several specific DNA motifs in the transcriptional regulation region of those activated genes. Taken together, we identified a conserved transcription activation domain in DYRK1 in urochordates and vertebrates. The activation is independent of the kinase activity of DYRK1 and can be repressed by its own N-terminal. Transcriptome and mutation data indicate that the transcriptional activation ability of HsDYRK1A is potentially involved in synaptic transmission and neuronal function related to the intellectual disability syndrome.
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Affiliation(s)
- Xiuke Ouyang
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhuqing Wang
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bingtong Wu
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiuxia Yang
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bo Dong
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laoshan Laboratory, Qingdao 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Correspondence:
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17
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Zhao X, Zhang H, Liu T, Zhao Y, Hu X, Liu S, Lin Y, Song B, He C. Transcriptome analysis provides StMYBA1 gene that regulates potato anthocyanin biosynthesis by activating structural genes. Front Plant Sci 2023; 14:1087121. [PMID: 36743487 PMCID: PMC9895859 DOI: 10.3389/fpls.2023.1087121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Anthocyanin biosynthesis is affected by light, temperature, and other environmental factors. The regulation mode of light on anthocyanin synthesis in apple, pear, tomato and other species has been reported, while not clear in potato. In this study, potato RM-210 tubers whose peel will turn purple gradually after exposure to light were selected. Transcriptome analysis was performed on RM-210 tubers during anthocyanin accumulation. The expression of StMYBA1 gene continued to increase during the anthocyanin accumulation in RM-210 tubers. Moreover, co-expression cluster analysis of differentially expressed genes showed that the expression patterns of StMYBA1 gene were highly correlated with structural genes CHS and CHI. The promoter activity of StMYBA1 was significantly higher in light conditions, and StMYBA1 could activate the promoter activity of structural genes StCHS, StCHI, and StF3H. Further gene function analysis found that overexpression of StMYBA1 gene could promote anthocyanin accumulation and structural gene expression in potato leaves. These results demonstrated that StMYBA1 gene promoted potato anthocyanin biosynthesis by activating the expression of structural genes under light conditions. These findings provide a theoretical basis and genetic resources for the regulatory mechanism of potato anthocyanin synthesis.
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Affiliation(s)
- Xijuan Zhao
- Engineering Research Center for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Huiling Zhang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Tengfei Liu
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yanan Zhao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Xinxi Hu
- Engineering Research Center for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Shengxuan Liu
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yuan Lin
- Engineering Research Center for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Botao Song
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Changzheng He
- Engineering Research Center for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, China
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18
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Li L, Zhang X, Yang H, Xu X, Chen Y, Dai D, Zhan S, Guo J, Zhong T, Wang L, Cao J, Zhang H. miR-193b-3p Promotes Proliferation of Goat Skeletal Muscle Satellite Cells through Activating IGF2BP1. Int J Mol Sci 2022; 23. [PMID: 36555418 DOI: 10.3390/ijms232415760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
As a well-known cancer-related miRNA, miR-193b-3p is enriched in skeletal muscle and dysregulated in muscle disease. However, the mechanism underpinning this has not been addressed so far. Here, we probed the impact of miR-193b-3p on myogenesis by mainly using goat tissues and skeletal muscle satellite cells (MuSCs), compared with mouse C2C12 myoblasts. miR-193b-3p is highly expressed in goat skeletal muscles, and ectopic miR-193b-3p promotes MuSCs proliferation and differentiation. Moreover, insulin-like growth factor-2 mRNA-binding protein 1 (IGF2BP1) is the most activated insulin signaling gene when there is overexpression of miR-193b-3p; the miRNA recognition element (MRE) within the IGF1BP1 3' untranslated region (UTR) is indispensable for its activation. Consistently, expression patterns and functions of IGF2BP1 were similar to those of miR-193b-3p in tissues and MuSCs. In comparison, ectopic miR-193b-3p failed to induce PAX7 expression and myoblast proliferation when there was IGF2BP1 knockdown. Furthermore, miR-193b-3p destabilized IGF2BP1 mRNA, but unexpectedly promoted levels of IGF2BP1 heteronuclear RNA (hnRNA), dramatically. Moreover, miR-193b-3p could induce its neighboring genes. However, miR-193b-3p inversely regulated IGF2BP1 and myoblast proliferation in the mouse C2C12 myoblast. These data unveil that goat miR-193b-3p promotes myoblast proliferation via activating IGF2BP1 by binding to its 3' UTR. Our novel findings highlight the positive regulation between miRNA and its target genes in muscle development, which further extends the repertoire of miRNA functions.
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19
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Kim S, Wengier DL, Ragland CJ, Sattely ES. Transcriptional Reactivation of Lignin Biosynthesis for the Heterologous Production of Etoposide Aglycone in Nicotiana benthamiana. ACS Synth Biol 2022; 11:3379-3387. [PMID: 36122905 PMCID: PMC9594330 DOI: 10.1021/acssynbio.2c00289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nicotiana benthamiana is a valuable plant chassis for heterologous production of medicinal plant natural products. This host is well suited for the processing of organelle-localized plant enzymes, and the conservation of the primary metabolism across the plant kingdom often provides required plant-specific precursor molecules that feed a given pathway. Despite this commonality in metabolism, limited precursor supply and/or competing host pathways can interfere with yields of heterologous products. Here, we use transient transcriptional reprogramming of endogenous N. benthamiana metabolism to drastically improve flux through the etoposide pathway derived from the medicinal plant Podophyllum spp. Specifically, coexpression of a single lignin-associated transcription factor, MYB85, with pathway genes results in unprecedented levels of heterologous product accumulation in N. benthamiana leaves: 1 mg/g dry weight (DW) of the etoposide aglycone, 35 mg/g DW (-)-deoxypodophyllotoxin, and 3.5 mg/g DW (-)-epipodophyllotoxin─up to two orders of magnitude above previously reported biosynthetic yields for the etoposide aglycone and eight times higher than what is observed for (-)-deoxypodophyllotoxin in the native medicinal plant. Unexpectedly, transient activation of lignin metabolism by transcription factor overexpression also reduces the production of undesired side products that likely result from competing N. benthamiana metabolism. Our work demonstrates that synthetic activation of lignin biosynthesis in leaf tissue is an effective strategy for optimizing the production of medicinal compounds derived from phenylpropanoid precursors in the plant chassis N. benthamiana. Furthermore, our results highlight the engineering value of MYB85, an early switch in lignin biosynthesis, for on-demand modulation of monolignol flux and support the role of MYB46 as a master regulator of lignin polymer deposition.
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Affiliation(s)
- Stacie
S. Kim
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Diego L. Wengier
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Carin J. Ragland
- Department
of Biology, Stanford University, Stanford, California 94305, United States
| | - Elizabeth S. Sattely
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States,Howard
Hughes Medical Institute, Stanford University, Stanford, California 94305, United States,
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20
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Abstract
The long-term exposure of low levels of the fungicide, 2-phenylphenol (2-PP), to the environment presents a hazard to human and aquatic health. The cost and difficulty in large-scale production limit the use of existing sensors to detect 2-PP for applications such as personal protection and persistent environmental monitoring of large areas. While advances have been made in using whole cells as biosensors for specific chemical detection, a whole-cell biosensor system with robust biocontainment for field deployment and a strong visual reporter for readouts in the deployed environment has yet to be realized. Here, engineered biosensors in an encapsulated and deployable system (eBEADS) were created to demonstrate a portable, no-power living sensor for detection of 2-PP in the environment. A whole-cell living sensor to detect 2-PP was developed in Escherichia coli by utilizing the 2-PP degradation pathway with an agenetic amplification circuit to produce a visual colorimetric output. To enable field deployment, a physical biocontainment system comprising polyacrylamide alginate beads was designed to encapsulate sensor strains, support long-term viability without supplemental nutrients, and allow permeability of the target analyte. Integration of materials and sensing strains has led to the development of a potential deployable end-to-end living sensor that, with the addition of an amplification circuit, has up to a 66-fold increase in β-galactosidase reporter output over non-amplified strains, responding to as little as 1 μM 2-PP while unencapsulated and 10 μM 2-PP while encapsulated. eBEADS enable sensitive and specific in-field detection of environmental perturbations and chemical threats without electronics.
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Affiliation(s)
- Brooke Luisi
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel 20723, Maryland, United States
| | - Rachel Hegab
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel 20723, Maryland, United States
| | - Chanel Person
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel 20723, Maryland, United States
| | - Kevin Seo
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel 20723, Maryland, United States
| | - Julie Gleason
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel 20723, Maryland, United States
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21
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Ghose AK, Abdullah SNA, Md Hatta MA, Megat Wahab PE. DNA Free CRISPR/DCAS9 Based Transcriptional Activation System for UGT76G1 Gene in Stevia rebaudiana Bertoni Protoplasts. Plants (Basel) 2022; 11:2393. [PMID: 36145794 PMCID: PMC9501275 DOI: 10.3390/plants11182393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
The UDP-glycosyltransferase 76G1 (UGT76G1) is responsible for the conversion of stevioside to rebaudioside A. Four single guide RNAs (sgRNAs) were designed from the UGT76G1 proximal promoter region of stevia by using the online-based tool, benchling. The dCas9 fused with VP64 as a transcriptional activation domain (TAD) was produced and purified for the formation of ribonucleoproteins (RNPs) by mixing with the in vitro transcribed sgRNAs. Protoplast yield was the highest from leaf mesophyll of in vitro grown stevia plantlets (3.16 × 106/g of FW) using ES5 (1.25% cellulase R-10 and 0.75% macerozyme R-10). The RNPs were delivered into the isolated protoplasts through the Polyethylene glycol (PEG)-mediated transfection method. The highest endogenous activation of the UGT76G1 gene was detected at 27.51-fold after 24 h of transfection with RNP30 consisting of CRISPR/dCas9-TAD with sgRNA30 and a similar activation level was obtained using RNP18, RNP33, and RNP34, produced using sgRNA18, sgRNA33, and sgRNA34, respectively. Activation of UGT76G1 by RNP18 led to a significant increase in the expression of the rate-limiting enzyme UGT85C2 by 2.37-fold and there was an increasing trend in the expression of UGT85C2 using RNP30, RNP33, and RNP34. Successful application of CRISPR/dCas9-TAD RNP in activating specific genes can avoid the negative integration effects of introduced DNA in the host genome.
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Affiliation(s)
- Asish Kumar Ghose
- Laboratory of Agronomy and Sustainable Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Biotechnology Division, Bangladesh Sugarcrop Research Institute, Ishurdi, Pabna 6620, Bangladesh
| | - Siti Nor Akmar Abdullah
- Laboratory of Agronomy and Sustainable Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Muhammad Asyraf Md Hatta
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Puteri Edaroyati Megat Wahab
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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22
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Hu Y, Xu J, Gao R, Xu Y, Huangfu B, Asakiya C, Huang X, Zhang F, Huang K, He X, Luo Y. Diallyl Trisulfide Prevents Adipogenesis and Lipogenesis by Regulating the Transcriptional Activation Function of KLF15 on PPARγ to Ameliorate Obesity. Mol Nutr Food Res 2022; 66:e2200173. [PMID: 35983694 DOI: 10.1002/mnfr.202200173] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/19/2022] [Indexed: 11/11/2022]
Abstract
SCOPE Diallyl trisulfide (DATS) is a bioactive compound in garlic. The anti-obesity effect of garlic oil has been reported, but the role and mechanism of DATS in preventing obesity remain to be explored. METHODS AND RESULTS We performed studies with high-fat-diet-induced obese mice and 3T3-L1 adipocytes. The results showed that DATS significantly reduced lipid accumulation and repaired disordered metabolism in vivo by restraining adipogenesis and lipogenesis, and promoting lipolysis and fatty acid oxidation in white adipose tissue. In cells, DATS played different roles at different stages of adipocyte differentiation. Notably, DATS reduced lipid accumulation mainly by inhibiting adipogenesis and lipogenesis at the late stage. KLF15 was knocked down in 3T3-L1 cells, which eliminated the inhibitory effect of DATS on adipogenesis and lipogenesis. The dual-luciferase reporter and ChIP assays indicated that DATS could inhibit the transcriptional activation function of KLF15 on PPARγ by inhibiting the binding of KLF15 to PPARγ promoter. The function comparison of structural analogs and the intervention of dithiothreitol showed that disulfide bond was crucial for DATS to work. CONCLUSION DATS prevents obesity by regulating the transcriptional activation function of KLF15 on PPARγ. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yanzhou Hu
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Jia Xu
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Ruxin Gao
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Ye Xu
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Bingxin Huangfu
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Charles Asakiya
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Xianghui Huang
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Feng Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), The Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing, 100083, P. R. China
| | - Xiaoyun He
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), The Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing, 100083, P. R. China
| | - Yunbo Luo
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), The Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing, 100083, P. R. China
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23
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Zheng L, Qiu B, Su L, Wang H, Cui X, Ge F, Liu D. Panax notoginseng WRKY Transcription Factor 9 Is a Positive Regulator in Responding to Root Rot Pathogen Fusarium solani. Front Plant Sci 2022; 13:930644. [PMID: 35909719 PMCID: PMC9331302 DOI: 10.3389/fpls.2022.930644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Panax notoginseng (Burk) F.H. Chen is a rare and valuable Chinese herb, but root rot mainly caused by Fusarium solani severely affects the yield and quality of P. notoginseng herbal materials. In this study, we isolated 30 P. notoginseng WRKY transcription factors (TFs), which were divided into three groups (I, II, and III) on the basis of a phylogenetic analysis. The expression levels of 10 WRKY genes, including PnWRKY9, in P. notoginseng roots increased in response to a methyl jasmonate (MeJA) treatment and the following F. solani infection. Additionally, PnWRKY9 was functionally characterized. The PnWRKY9 protein was localized to the nucleus. The overexpression of PnWRKY9 in tobacco (Nicotiana tabacum) considerably increased the resistance to F. solani, whereas an RNAi-mediated decrease in the PnWRKY9 expression level in P. notoginseng leaves increased the susceptibility to F. solani. The RNA sequencing and hormone content analyses of PnWRKY9-overexpression tobacco revealed that PnWRKY9 and the jasmonic acid (JA) signaling pathway synergistically enhance disease resistance. The PnWRKY9 recombinant protein was observed to bind specifically to the W-box sequence in the promoter of a JA-responsive and F. solani resistance-related defensin gene (PnDEFL1). A yeast one-hybrid assay indicated that PnWRKY9 can activate the transcription of PnDEFL1. Furthermore, a co-expression assay in tobacco using β-glucuronidase (GUS) as a reporter further verified that PnWRKY9 positively regulates PnDEFL1 expression. Overall, in this study, we identified P. notoginseng WRKY TFs and demonstrated that PnWRKY9 positively affects plant defenses against the root rot pathogen. The data presented herein provide researchers with fundamental information regarding the regulatory mechanism mediating the coordinated activities of WRKY TFs and the JA signaling pathway in P. notoginseng responses to the root rot pathogen.
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Affiliation(s)
- Lilei Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
| | - Bingling Qiu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
| | - Linlin Su
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
| | - Hanlin Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
| | - Feng Ge
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
| | - Diqiu Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
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24
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Zeng H, Xu H, Wang H, Chen H, Wang G, Bai Y, Wei Y, Shi H. LSD3 mediates the oxidative stress response through fine-tuning APX2 activity and the NF-YC15-GSTs module in cassava. Plant J 2022; 110:1447-1461. [PMID: 35352421 DOI: 10.1111/tpj.15749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/12/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Reactive oxygen species (ROS) overproduction leads to oxidative damage under almost all stress conditions. Lesion-Simulating Disease (LSD), a zinc finger protein, is an important negative regulator of ROS accumulation and cell death in plants. However, the in vivo role of LSD in cassava (Manihot esculenta) and the underlying molecular mechanisms remain elusive. Here, we found that MeLSD3 is essential for the oxidative stress response in cassava. MeLSD3 physically interacted with ascorbate peroxidase 2 (MeAPX2), thereby promoting its enzymatic activity. In addition, MeLSD3 also interacted with the nuclear factor YC15 (MeNF-YC15), which also interacted with nuclear factor YA2/4 (MeNF-YA2/4) and nuclear factor YB18 (MeNF-YB18) to form an MeNF-YC15-MeNF-YA2/4-MeNF-YB18 complex. Notably, MeLSD3 positively modulated the transcriptional activation of the MeNF-YC15-MeNF-YA2/4-MeNF-YB18 complex by interacting with the CCAAT boxes of the promoters of glutathione S-transferases U37/U39 (MeGST-U37/U39), activating their transcription. When one or both of MeLSD3 and the MeNF-YC15-MeNF-YA2/4-MeNF-YB18 complex were co-silenced, cassava showed decreased oxidative stress resistance, while overexpression of MeGST-U37/U39 alleviated the oxidative stress-sensitive phenotype of these silenced plants. This study illustrates the dual roles of MeLSD3 in promoting MeAPX2 activity and MeNF-YC15-MeGST-U37/U39 regulation, which underlie the oxidative stress response in cassava.
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Affiliation(s)
- Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Haoran Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Hao Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Hao Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Guanqi Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Yujing Bai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
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25
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Wei Q, Liu Y, Lan K, Wei X, Hu T, Chen R, Zhao S, Yin X, Xie T. Identification and Analysis of MYB Gene Family for Discovering Potential Regulators Responding to Abiotic Stresses in Curcuma wenyujin. Front Genet 2022; 13:894928. [PMID: 35547255 PMCID: PMC9081655 DOI: 10.3389/fgene.2022.894928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
MYB superfamily is one of the most abundant families in plants, and plays critical role in plant growth, development, metabolism regulation, and stress response. Curcuma wenyujin is the main source plant of three traditional Chinese medicines, which are widely used in clinical treatment due to its diverse pharmacological activities. In present study, 88 CwMYBs were identified and analyzed in C. wenyujin, including 43 MYB-related genes, 42 R2R3-MYB genes, two 3R-MYB genes, and one 4R-MYB gene. Forty-three MYB-related proteins were classified into several types based on conserved domains and specific motifs, including CCA1-like type, R-R type, Myb-CC type, GARP-like type, and TBR-like type. The analysis of motifs in MYB DBD and no-MYB regions revealed the relevance of protein structure and function. Comparative phylogeny analysis divided 42 R2R3-MYB proteins into 19 subgroups and provided a reference for understanding the functions of some CwMYBs based on orthologs of previously characterized MYBs. Expression profile analysis of CwMYB genes revealed the differentially expressed genes responding to various abiotic stresses. Four candidate MYB genes were identified by combining the results of phylogeny analysis and expression analysis. CwMYB10, CwMYB18, CwMYB39, and CwMYB41 were significantly induced by cold, NaCl, and MeJA stress treatments. CwMYB18 and CwMYB41 were proved as regulators with activity of transcriptional activation, whereas CwMYB39 and CwMYB10 were not. They may participate in the response to abiotic stresses through different mechanisms in C. wenyujin. This study was the first step toward understanding the CwMYB family and the response to abiotic stresses in C. wenyujin.
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Affiliation(s)
- Qiuhui Wei
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Yuyang Liu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Kaer Lan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Xin Wei
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Tianyuan Hu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Rong Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Shujuan Zhao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Xiaopu Yin
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
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26
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Tchurikov NA, Klushevskaya ES, Alembekov IR, Bukreeva AS, Kretova AN, Chechetkin VR, Kravatskaya GI, Kravatsky YV. Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs. Int J Mol Sci 2022; 23:ijms23063014. [PMID: 35328433 PMCID: PMC8954558 DOI: 10.3390/ijms23063014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
Small noncoding RNAs of different origins and classes play several roles in the regulation of gene expression. Here, we show that diverged and rearranged fragments of rDNA units are scattered throughout the human genome and that endogenous small noncoding RNAs are processed by the Microprocessor complex from specific regions of ribosomal RNAs shaping hairpins. These small RNAs correspond to particular sites inside the fragments of rDNA that mostly reside in intergenic regions or the introns of about 1500 genes. The targets of these small ribosomal RNAs (srRNAs) are characterized by a set of epigenetic marks, binding sites of Pol II, RAD21, CBP, and P300, DNase I hypersensitive sites, and by enrichment or depletion of active histone marks. In HEK293T cells, genes that are targeted by srRNAs (srRNA target genes) are involved in differentiation and development. srRNA target genes are enriched with more actively transcribed genes. Our data suggest that remnants of rDNA sequences and srRNAs may be involved in the upregulation or downregulation of a specific set of genes in human cells. These results have implications for diverse fields, including epigenetics and gene therapy.
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Affiliation(s)
- Nickolai A. Tchurikov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Correspondence:
| | - Elena S. Klushevskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Ildar R. Alembekov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Anastasiia S. Bukreeva
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Antonina N. Kretova
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Vladimir R. Chechetkin
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Galina I. Kravatskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Yuri V. Kravatsky
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
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Zhou M, Chen JY, Chao ML, Zhang C, Shi ZG, Zhou XC, Xie LP, Sun SX, Huang ZR, Luo SS, Ji Y. S-nitrosylation of c-Jun N-terminal kinase mediates pressure overload-induced cardiac dysfunction and fibrosis. Acta Pharmacol Sin 2022; 43:602-612. [PMID: 34011968 PMCID: PMC8888706 DOI: 10.1038/s41401-021-00674-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/31/2021] [Indexed: 02/04/2023] Open
Abstract
Cardiac fibrosis (CF) is an irreversible pathological process that occurs in almost all kinds of cardiovascular diseases. Phosphorylation-dependent activation of c-Jun N-terminal kinase (JNK) induces cardiac fibrosis. However, whether S-nitrosylation of JNK mediates cardiac fibrosis remains an open question. A biotin-switch assay confirmed that S-nitrosylation of JNK (SNO-JNK) increased significantly in the heart tissues of hypertrophic patients, transverse aortic constriction (TAC) mice, spontaneously hypertensive rats (SHRs), and neonatal rat cardiac fibroblasts (NRCFs) stimulated with angiotensin II (Ang II). Site to site substitution of alanine for cysteine in JNK was applied to determine the S-nitrosylated site. S-Nitrosylation occurred at both Cys116 and Cys163 and substitution of alanine for cysteine 116 and cysteine 163 (C116/163A) inhibited Ang II-induced myofibroblast transformation. We further confirmed that the source of S-nitrosylation was inducible nitric oxide synthase (iNOS). 1400 W, an inhibitor of iNOS, abrogated the profibrotic effects of Ang II in NRCFs. Mechanistically, SNO-JNK facilitated the nuclear translocation of JNK, increased the phosphorylation of c-Jun, and induced the transcriptional activity of AP-1 as determined by chromatin immunoprecipitation and EMSA. Finally, WT and iNOS-/- mice were subjected to TAC and iNOS knockout reduced SNO-JNK and alleviated cardiac fibrosis. Our findings demonstrate an alternative mechanism by which iNOS-induced SNO-JNK increases JNK pathway activity and accelerates cardiac fibrosis. Targeting SNO-JNK might be a novel therapeutic strategy against cardiac fibrosis.
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Affiliation(s)
- Miao Zhou
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Ji-yu Chen
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Meng-Lin Chao
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Chao Zhang
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Zhi-guang Shi
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Xue-chun Zhou
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Li-ping Xie
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203 China ,grid.89957.3a0000 0000 9255 8984Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Shi-xiu Sun
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Zheng-rong Huang
- grid.412625.6Department of Cardiology, the First Affiliated Hospital of Xiamen University, Xiamen, 361003 China
| | - Shan-shan Luo
- grid.89957.3a0000 0000 9255 8984Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203 China
| | - Yong Ji
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, 201203, China. .,Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 201203, China. .,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 201203, China.
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28
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Sanz AB, García R, Pavón-Vergés M, Rodríguez-Peña JM, Arroyo J. Control of Gene Expression via the Yeast CWI Pathway. Int J Mol Sci 2022; 23:ijms23031791. [PMID: 35163713 PMCID: PMC8836261 DOI: 10.3390/ijms23031791] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/18/2022] Open
Abstract
Living cells exposed to stressful environmental situations can elicit cellular responses that guarantee maximal cell survival. Most of these responses are mediated by mitogen-activated protein kinase (MAPK) cascades, which are highly conserved from yeast to humans. Cell wall damage conditions in the yeast Saccharomyces cerevisiae elicit rescue mechanisms mainly associated with reprogramming specific transcriptional responses via the cell wall integrity (CWI) pathway. Regulation of gene expression by this pathway is coordinated by the MAPK Slt2/Mpk1, mainly via Rlm1 and, to a lesser extent, through SBF (Swi4/Swi6) transcription factors. In this review, we summarize the molecular mechanisms controlling gene expression upon cell wall stress and the role of chromatin structure in these processes. Some of these mechanisms are also discussed in the context of other stresses governed by different yeast MAPK pathways. Slt2 regulates both transcriptional initiation and elongation by interacting with chromatin at the promoter and coding regions of CWI-responsive genes but using different mechanisms for Rlm1- and SBF-dependent genes. Since MAPK pathways are very well conserved in eukaryotic cells and are essential for controlling cellular physiology, improving our knowledge regarding how they regulate gene expression could impact the future identification of novel targets for therapeutic intervention.
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Xu Y, Wang D, Zhao G. Transcriptional activation of Proteasome 26S non-ATPase subunit 7 by forkhead box P3 participates in gastric cancer cell proliferation and apoptosis. Bioengineered 2022; 13:2525-2536. [PMID: 35037550 PMCID: PMC8974172 DOI: 10.1080/21655979.2021.2018097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Proteasome 26S non-ATPase subunit 7 (PSMD7) and forkhead box P3 (FOXP3) have been found to be both upregulated in gastric cancer tissues. FOXP3 was also predicted to have binding sites on PSMD7 promoter. Thus, this study investigated the relationship between PSMD7 and FOXP3 and their roles in gastric cancer. Bioinformatic databases predicted PSMD7 expression in non-cancerous gastric tissue and gastric cancer tissue, as well as the correlation between PSMD7 and the overall/disease free survival. PSMD7 expression in non-cancerous gastric tissue or cells and gastric cancer tissue or cells was detected by qPCR and Western blot. After PSMD7 downregulation by siRNA interference, cell viability, colony-forming capacity and cell apoptosis were analyzed with cell counting kit-8 assay, colony formation assay and terminal deoxynucleotidyl transferasemediated dUTP nick end-labeling. Proliferation and apoptosis markers were assayed by qPCR and Western blot. Dual-luciferase reporter and chromatin immunoprecipitation assays were performed to look at the binding relationship between FOXP3 and PSMD7 promoter. Cell proliferation and apoptosis were examined again after co-transfection of PSMD7 siRNA plasmid and FOXP3 overexpression plasmid. PSMD7 expression was much higher in gastric cancer tissue and cell lines. Interference with PSMD7 decreased gastric cancer cell viability, inhibited their proliferation and colony formation and promoted cell apoptosis. FOXP3 was found to bind to PSMD7 promoter and activate PSMD7 expression. Overexpression of FOXP3 could rescue the effects of PSMD7 knockdown on gastric cancer cells. PSMD7 is involved in the proliferation and apoptosis of gastric cancer cells and can be transcriptionally regulated by FOXP3.
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Affiliation(s)
- Yujie Xu
- Department of Gastrointestinal Surgery, Haikou People's Hospital, Haikou, Hainan Province, China
| | - Dingmao Wang
- Department of Gastrointestinal Surgery, Haikou People's Hospital, Haikou, Hainan Province, China
| | - Guodong Zhao
- Department of Gastrointestinal Surgery, Haikou People's Hospital, Haikou, Hainan Province, China
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30
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Ren C, Li H, Liu Y, Li S, Liang Z. Highly efficient activation of endogenous gene in grape using CRISPR/dCas9-based transcriptional activators. Hortic Res 2022; 9:uhab037. [PMID: 35039855 PMCID: PMC8807946 DOI: 10.1093/hr/uhab037] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/18/2022] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
Overexpression and knockout (or knockdown) of gene of interest are two commonly used strategies for gene functional study. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system-mediated gene knockout had been applied in most plant species, including grapevine. However, CRISPR/dCas9 (deactivated Cas9)-based transcriptional activation is still unreported in fruit crops, although a few studies had been documented in Arabidopsis and rice. Here, we tested two transcriptional activators VP64 and TV for transcriptional activation of endogenous genes in grape. Both the dCas9-VP64 and dCas9-TV systems are efficient enough for transcriptional activation of the UDP-glucose flavonoid glycosyltransferases (UFGT) gene in grape cells. The effectiveness of the dCas9-VP64 system in UFGT activation was about 1.6- to 5.6-fold, while the efficiency of the dCas9-TV system was around 5.7- to 7.2-fold. Moreover, in grapevine plants, highly efficient activation of the cold-responsive transcription factor gene CBF4 was achieved by using the dCas9-TV system. The expression of CBF4 was increased 3.7- to 42.3-fold in transgenic plants. Compared with the wild-type plants, the CBF4-activated plants exhibited lower electrolyte leakage after cold treatment. Our results demonstrate the effectiveness of the dCas9-VP64 and dCas9-TV system in gene activation in grape, which will facilitate application of transcriptional activation in this economically important species.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- University of Chinese Academy of Sciences,
19 Yuquan Rd, Beijing 100049, China
| | - Yanfei Liu
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- University of Chinese Academy of Sciences,
19 Yuquan Rd, Beijing 100049, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
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31
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Wang P, Yan Y, Bai Y, Dong Y, Wei Y, Zeng H, Shi H. Phosphorylation of RAV1/2 by KIN10 is essential for transcriptional activation of CAT6/7, which underlies oxidative stress response in cassava. Cell Rep 2021; 37:110119. [PMID: 34910906 DOI: 10.1016/j.celrep.2021.110119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/11/2021] [Accepted: 11/18/2021] [Indexed: 01/17/2023] Open
Abstract
Related to ABI3/VP1 (RAV) transcription factors have important roles in plant stress responses; however, it is unclear whether RAVs regulates oxidative stress response in cassava (Manihot esculenta). In this study, we report that MeRAV1/2 positively regulate oxidative stress resistance and catalase (CAT) activity in cassava. Consistently, RNA sequencing (RNA-seq) identifies three MeCATs that are differentially expressed in MeRAV1/2-silenced cassava leaves. Interestingly, MeCAT6 and MeCAT7 are identified as direct transcriptional targets of MeRAV1/2 via binding to their promoters. In addition, protein kinase MeKIN10 directly interacts with MeRAV1/2 to phosphorylate them at Ser45 and Ser44 residues, respectively, to promote their direct transcriptional activation on MeCAT6 and MeCAT7. Site mutation of MeRAV1S45A or MeRAV2S44A has no significant effect on the activities of MeCAT6 and MeCAT7 promoters or on oxidative stress resistance. In summary, this study demonstrates that the phosphorylation of MeRAV1/2 by MeKIN10 is essential for its direct transcriptional activation of MeCAT6/7 in response to oxidative stress.
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Affiliation(s)
- Peng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan 570228, China
| | - Yu Yan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan 570228, China
| | - Yujing Bai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan 570228, China
| | - Yabin Dong
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan 570228, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan 570228, China
| | - Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan 570228, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan 570228, China.
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32
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Hu Y, Romão E, Vincke C, Brys L, Elkrim Y, Vandevenne M, Liu C, Muyldermans S. Intrabody Targeting HIF-1α Mediates Transcriptional Downregulation of Target Genes Related to Solid Tumors. Int J Mol Sci 2021; 22:12335. [PMID: 34830219 DOI: 10.3390/ijms222212335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/17/2022] Open
Abstract
Uncontrolled growth of solid tumors will result in a hallmark hypoxic condition, whereby the key transcriptional regulator of hypoxia inducible factor-1α (HIF-1α) will be stabilized to activate the transcription of target genes that are responsible for the metabolism, proliferation, and metastasis of tumor cells. Targeting and inhibiting the transcriptional activity of HIF-1 may provide an interesting strategy for cancer therapy. In the present study, an immune library and a synthetic library were constructed for the phage display selection of Nbs against recombinant PAS B domain protein (rPasB) of HIF-1α. After panning and screening, seven different nanobodies (Nbs) were selected, of which five were confirmed via immunoprecipitation to target the native HIF-1α subunit. The inhibitory effect of the selected Nbs on HIF-1 induced activation of target genes has been evaluated after intracellular expression of these Nbs in HeLa cells. The dramatic inhibition of both intrabody formats on the expression of HIF-1-related target genes has been confirmed, which indicated the inhibitory efficacy of selected Nbs on the transcriptional activity of HIF-1.
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El Kharraz S, Dubois V, van Royen ME, Houtsmuller AB, Pavlova E, Atanassova N, Nguyen T, Voet A, Eerlings R, Handle F, Prekovic S, Smeets E, Moris L, Devlies W, Ohlsson C, Poutanen M, Verstrepen KJ, Carmeliet G, Launonen KM, Helminen L, Palvimo JJ, Libert C, Vanderschueren D, Helsen C, Claessens F. The androgen receptor depends on ligand-binding domain dimerization for transcriptional activation. EMBO Rep 2021; 22:e52764. [PMID: 34661369 DOI: 10.15252/embr.202152764] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/28/2023] Open
Abstract
Whereas dimerization of the DNA-binding domain of the androgen receptor (AR) plays an evident role in recognizing bipartite response elements, the contribution of the dimerization of the ligand-binding domain (LBD) to the correct functioning of the AR remains unclear. Here, we describe a mouse model with disrupted dimerization of the AR LBD (ARLmon/Y ). The disruptive effect of the mutation is demonstrated by the feminized phenotype, absence of male accessory sex glands, and strongly affected spermatogenesis, despite high circulating levels of testosterone. Testosterone replacement studies in orchidectomized mice demonstrate that androgen-regulated transcriptomes in ARLmon/Y mice are completely lost. The mutated AR still translocates to the nucleus and binds chromatin, but does not bind to specific AR binding sites. In vitro studies reveal that the mutation in the LBD dimer interface also affects other AR functions such as DNA binding, ligand binding, and co-regulator binding. In conclusion, LBD dimerization is crucial for the development of AR-dependent tissues through its role in transcriptional regulation in vivo. Our findings identify AR LBD dimerization as a possible target for AR inhibition.
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Affiliation(s)
- Sarah El Kharraz
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Vanessa Dubois
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | | | | | - Ekatarina Pavlova
- Institute of Experimental Morphology Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nina Atanassova
- Institute of Experimental Morphology Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tien Nguyen
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Arnout Voet
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Roy Eerlings
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Florian Handle
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Stefan Prekovic
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elien Smeets
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Lisa Moris
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Wout Devlies
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | - Matti Poutanen
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden.,Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology and KU Leuven Laboratory for Genetics and Genomics, VIB - KU Leuven Center for Microbiology, Leuven, Belgium
| | - Geert Carmeliet
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | | | - Laura Helminen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Claude Libert
- VIB Center for Inflammation Research, VIB, Ghent, Belgium.,Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Christine Helsen
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frank Claessens
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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34
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Liu C, Wang N, Luo R, Li L, Yang W, Wang X, Shen M, Wu Q, Gong C. A programmable hierarchical-responsive nanoCRISPR elicits robust activation of endogenous target to treat cancer. Theranostics 2021; 11:9833-9846. [PMID: 34815789 PMCID: PMC8581410 DOI: 10.7150/thno.62449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/24/2021] [Indexed: 02/05/2023] Open
Abstract
Despite promising progress of cancer gene therapy made, these therapeutics were still limited by the diversity of gene sizes and types. CRISPR/dCas9 mediated activation of tumor endogenous gene has shown great potential to surmount hinders of genetic varieties during the process of cancer gene therapy. However, the blood interference along with complicated tumor extra/intracellular microenvironment substantially compromise the performance of CRISPR/dCas9-based therapeutics in vivo. Methods: In this study, we constructed a programmable hierarchical-responsive nanoCRISPR (PICASSO) that can achieve sequential responses to the multiple physiological barriers in vivo. The core-shell structure endows PICASSO with long blood circulation capacity and tumor target accumulation as well as efficient cellular uptake and lysosomal escape, leading to high-performance of CRISPR/dCas9-mediated gene activation, which favors the antitumor efficacy. Results: Owing to these properties, PICASSO facilitated CRISPR/dCas9 mediated efficient transcriptional activation of various types of endogenous gene, and long non-protein-coding genes (LncRNA) containing targets ranging in size from ~1 kb to ~2000 kb in tumor cells. Intravenous administration of PICASSO to the tumor-bearing mice can achieve effective transcriptional activation of therapeutic endogenous gene, resulting in remarkable CRISPR/dCas9-mediate tumor inhibition with minimal adverse effect. Conclusions: Taken together, these characteristics allow PICASSO to unleash the potential of CRISPR/dCas9-based therapeutics in oncological treatment. The study provides a simple and versatile strategy to break through the restriction of sizes and types against cancer by utilization of tumor endogenous gene.
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Affiliation(s)
| | | | | | | | | | | | | | - Qinjie Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital Sichuan University, Chengdu, 610041, P. R. China
| | - Changyang Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital Sichuan University, Chengdu, 610041, P. R. China
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35
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Yu F, Li S, Chen H, Hao K, Meng L, Yang J, Zhao Z. Multiple AT-rich sequences function as a cis-element in the ORF3 promoter in channel catfish virus (Ictaluridherpesvirus 1). J Fish Dis 2021; 44:1609-1617. [PMID: 34192354 DOI: 10.1111/jfd.13483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The expression of herpesvirus genes during infection of tissue culture cells can be classified into three main classes: immediate-early (IE), early and late. The transcriptional regulation of herpesvirus IE genes is a critical regulatory step in the initiation of viral infection, with their regulation differing from that of early and late genes. Herein, we report that an IE gene (ORF3) promoter in channel catfish virus (CCV, Ictalurid herpesvirus 1) can be activated regardless of the presence or absence of CCV infection, indicating that the ORF3 promoter is efficiently driven by host-cell transcription factors in a viral infection-independent manner. The analysis of truncated promoter activity suggested that several transcription elements play a role in activating the ORF3 promoter, with the key cis-elements seemingly located in the flanking sequence of the start codon ATG. We further found that this flanking sequence contained multiple AT-rich sequences, and systematic mutational analyses showed that these AT-rich sequences affected normal transcription levels of the ORF3 promoter. To summarize, multiple AT-rich domains, representing the novel architecture of IE gene promoters in Ictalurid herpesvirus 1, serve as a cis-element for ORF3 transcription.
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Affiliation(s)
- Fei Yu
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Shuxin Li
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Hongxun Chen
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Kai Hao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Lihui Meng
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jiayue Yang
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
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36
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Soshnikova N, Tatarskiy E, Tatarskiy V, Klimenko N, Shtil AA, Nikiforov M, Georgieva S. PHF10 subunit of PBAF complex mediates transcriptional activation by MYC. Oncogene 2021; 40:6071-6080. [PMID: 34465901 PMCID: PMC8863208 DOI: 10.1038/s41388-021-01994-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/24/2021] [Accepted: 08/10/2021] [Indexed: 02/08/2023]
Abstract
The PBAF complex, a member of SWI/SNF family of chromatin remodelers, plays an essential role in transcriptional regulation. We revealed a disease progression associated elevation of PHF10 subunit of PBAF in clinical melanoma samples. In melanoma cell lines, PHF10 interacts with MYC and facilitates the recruitment of PBAF complex to target gene promoters, therefore, augmenting MYC transcriptional activation of genes involved in the cell cycle progression. Depletion of either PHF10 or MYC induced G1 accumulation and a senescence-like phenotype. Our data identify PHF10 as a pro-oncogenic mechanism and an essential novel link between chromatin remodeling and MYC-dependent gene transcription.
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Affiliation(s)
- N.V. Soshnikova
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia,Corresponding authors: (N.V.Soshnikova); (S.G.Georgieva)
| | - E.V. Tatarskiy
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - V.V. Tatarskiy
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - N.S. Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - A. A. Shtil
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - M.A. Nikiforov
- Department of Cancer Biology, Wake Forest University, Medical Center Drive, Winston-Salem, NC 27101, USA
| | - S.G. Georgieva
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia,Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia,Corresponding authors: (N.V.Soshnikova); (S.G.Georgieva)
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Abstract
Breast cancer (BC) is the most ubiquitous cancer in women. Approximately 70–80% of BC diagnoses are positive for estrogen receptor (ER) alpha (ERα). The steroid hormone estrogen [17β-estradiol (E2)] plays a vital role both in the initiation and progression of BC. The E2-ERα mediated actions involve genomic signaling and non-genomic signaling. The specificity and magnitude of ERα signaling are mediated by interactions between ERα and several coregulator proteins called coactivators or corepressors. Alterations in the levels of coregulators are common during BC progression and they enhance ligand-dependent and ligand-independent ERα signaling which drives BC growth, progression, and endocrine therapy resistance. Many ERα coregulator proteins function as scaffolding proteins and some have intrinsic or associated enzymatic activities, thus the targeting of coregulators for blocking BC progression is a challenging task. Emerging data from in vitro and in vivo studies suggest that targeting coregulators to inhibit BC progression to therapy resistance is feasible. This review explores the current state of ERα coregulator signaling and the utility of targeting the ERα coregulator axis in treating advanced BC.
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Affiliation(s)
- Kristin A Altwegg
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA.,Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Ratna K Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA.,Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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38
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Li S, Liu G, Pu L, Liu X, Wang Z, Zhao Q, Chen H, Ge F, Liu D. WRKY Transcription Factors Actively Respond to Fusarium oxysporum in Lilium regale. Phytopathology 2021; 111:1625-1637. [PMID: 33576690 DOI: 10.1094/phyto-10-20-0480-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The WRKY transcription factors form a plant-specific superfamily important for regulating plant development, stress responses, and hormone signal transduction. In this study, many WRKY genes (LrWRKY1-35) were identified in Lilium regale, which is a wild lily species highly resistant to Fusarium wilt. These WRKY genes were divided into three classes (I to III) based on a phylogenetic analysis. The Class-II WRKY transcription factors were further divided into five subclasses (IIa, IIb, IIc, IId, and IIe). Moreover, the gene expression patterns based on a quantitative real-time PCR analysis revealed the WRKY genes were differentially expressed in the L. regale roots, stems, leaves, and flowers. Additionally, the expression of the WRKY genes was affected by an infection by Fusarium oxysporum as well as by salicylic acid, methyl jasmonate, ethephon, and hydrogen peroxide treatments. Moreover, the LrWRKY1 protein was localized to the nucleus of onion epidermal cells. The recombinant LrWRKY1 protein purified from Escherichia coli bound specifically to DNA fragments containing the W-box sequence, and a yeast one-hybrid assay indicated that LrWRKY1 can activate transcription. A co-expression assay in tobacco (Nicotiana tabacum) confirmed LrWRKY1 regulates the expression of LrPR10-5. Furthermore, the overexpression of LrWRKY1 in tobacco and the Oriental hybrid 'Siberia' (susceptible to F. oxysporum) increased the resistance of the transgenic plants to F. oxysporum. Overall, LrWRKY1 regulates the expression of the resistance gene LrPR10-5 and is involved in the defense response of L. regale to F. oxysporum. This study provides valuable information regarding the expression and functional characteristics of L. regale WRKY genes.
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Affiliation(s)
- Shan Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Guanze Liu
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Limei Pu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xuyan Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Zie Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Qin Zhao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Hongjun Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Feng Ge
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Diqiu Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
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Lee JH, Wang R, Xiong F, Krakowiak J, Liao Z, Nguyen PT, Moroz-Omori EV, Shao J, Zhu X, Bolt MJ, Wu H, Singh PK, Bi M, Shi CJ, Jamal N, Li G, Mistry R, Jung SY, Tsai KL, Ferreon JC, Stossi F, Caflisch A, Liu Z, Mancini MA, Li W. Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Mol Cell 2021; 81:3368-3385.e9. [PMID: 34375583 PMCID: PMC8383322 DOI: 10.1016/j.molcel.2021.07.024] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 06/10/2021] [Accepted: 07/20/2021] [Indexed: 01/22/2023]
Abstract
The mechanistic understanding of nascent RNAs in transcriptional control remains limited. Here, by a high sensitivity method methylation-inscribed nascent transcripts sequencing (MINT-seq), we characterized the landscapes of N6-methyladenosine (m6A) on nascent RNAs. We uncover heavy but selective m6A deposition on nascent RNAs produced by transcription regulatory elements, including promoter upstream antisense RNAs and enhancer RNAs (eRNAs), which positively correlates with their length, inclusion of m6A motif, and RNA abundances. m6A-eRNAs mark highly active enhancers, where they recruit nuclear m6A reader YTHDC1 to phase separate into liquid-like condensates, in a manner dependent on its C terminus intrinsically disordered region and arginine residues. The m6A-eRNA/YTHDC1 condensate co-mixes with and facilitates the formation of BRD4 coactivator condensate. Consequently, YTHDC1 depletion diminished BRD4 condensate and its recruitment to enhancers, resulting in inhibited enhancer and gene activation. We propose that chemical modifications of eRNAs together with reader proteins play broad roles in enhancer activation and gene transcriptional control.
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Affiliation(s)
- Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Ruoyu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX 77030, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Joanna Krakowiak
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Zian Liao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX 77030, USA
| | - Phuoc T Nguyen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX 77030, USA
| | - Elena V Moroz-Omori
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jiaofang Shao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Xiaoyu Zhu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Michael J Bolt
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA; Gulf Coast Consortia Center for Advanced Microscopy and Image Informatics, Houston, TX 77030, USA
| | - Haoyi Wu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX 77030, USA
| | - Pankaj K Singh
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA; Gulf Coast Consortia Center for Advanced Microscopy and Image Informatics, Houston, TX 77030, USA
| | - Mingjun Bi
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Caleb J Shi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Naadir Jamal
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Guojie Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Ragini Mistry
- Gulf Coast Consortia Center for Advanced Microscopy and Image Informatics, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Gulf Coast Consortia Center for Advanced Microscopy and Image Informatics, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Michael A Mancini
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA; Gulf Coast Consortia Center for Advanced Microscopy and Image Informatics, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX 77030, USA.
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40
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Miao X, Niibe K, Zhang M, Liu Z, Nattasit P, Ohori-Morita Y, Nakamura T, Jiang X, Egusa H. Stage-Specific Role of Amelx Activation in Stepwise Ameloblast Induction from Mouse Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:ijms22137195. [PMID: 34281250 PMCID: PMC8268366 DOI: 10.3390/ijms22137195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/27/2021] [Accepted: 06/27/2021] [Indexed: 01/29/2023] Open
Abstract
Amelogenin comprises ~90% of enamel proteins; however, the involvement of Amelx transcriptional activation in regulating ameloblast differentiation from induced pluripotent stem cells (iPSCs) remains unknown. In this study, we generated doxycycline-inducible Amelx-expressing mouse iPSCs (Amelx-iPSCs). We then established a three-stage ameloblast induction strategy from Amelx-iPSCs, including induction of surface ectoderm (stage 1), dental epithelial cells (DECs; stage 2), and ameloblast lineage (stage 3) in sequence, by manipulating several signaling molecules. We found that adjunctive use of lithium chloride (LiCl) in addition to bone morphogenetic protein 4 and retinoic acid promoted concentration-dependent differentiation of DECs. The resulting cells had a cobblestone appearance and keratin14 positivity. Attenuation of LiCl at stage 3 together with transforming growth factor β1 and epidermal growth factor resulted in an ameloblast lineage with elongated cell morphology, positivity for ameloblast markers, and calcium deposition. Although stage-specific activation of Amelx did not produce noticeable phenotypic changes in ameloblast differentiation, Amelx activation at stage 3 significantly enhanced cell adhesion as well as decreased proliferation and migration. These results suggest that the combination of inducible Amelx transcription and stage-specific ameloblast induction for iPSCs represents a powerful tool to highlight underlying mechanisms in ameloblast differentiation and function in association with Amelx expression.
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Affiliation(s)
- Xinchao Miao
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
| | - Kunimichi Niibe
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
- Correspondence: (K.N.); (H.E.); Tel.: +81-22-717-8363 (K.N.); +81-22-717-8363 (H.E.)
| | - Maolin Zhang
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
- Department of Prosthodontics, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China;
| | - Zeni Liu
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Praphawi Nattasit
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
| | - Yumi Ohori-Morita
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
| | - Takashi Nakamura
- Division of Molecular Pharmacology and Cell Biophysics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan;
| | - Xinquan Jiang
- Department of Prosthodontics, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China;
| | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan
- Correspondence: (K.N.); (H.E.); Tel.: +81-22-717-8363 (K.N.); +81-22-717-8363 (H.E.)
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Ko MS, Yun JY, Baek IJ, Jang JE, Hwang JJ, Lee SE, Heo SH, Bader DA, Lee CH, Han J, Moon JS, Lee JM, Hong EG, Lee IK, Kim SW, Park JY, Hartig SM, Kang UJ, Moore DD, Koh EH, Lee KU. Mitophagy deficiency increases NLRP3 to induce brown fat dysfunction in mice. Autophagy 2021; 17:1205-1221. [PMID: 32400277 PMCID: PMC8143238 DOI: 10.1080/15548627.2020.1753002] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/24/2020] [Accepted: 04/03/2020] [Indexed: 12/22/2022] Open
Abstract
Although macroautophagy/autophagy deficiency causes degenerative diseases, the deletion of essential autophagy genes in adipocytes paradoxically reduces body weight. Brown adipose tissue (BAT) plays an important role in body weight regulation and metabolic control. However, the key cellular mechanisms that maintain BAT function remain poorly understood. in this study, we showed that global or brown adipocyte-specific deletion of pink1, a Parkinson disease-related gene involved in selective mitochondrial autophagy (mitophagy), induced BAT dysfunction, and obesity-prone type in mice. Defective mitochondrial function is among the upstream signals that activate the NLRP3 inflammasome. NLRP3 was induced in brown adipocyte precursors (BAPs) from pink1 knockout (KO) mice. Unexpectedly, NLRP3 induction did not induce canonical inflammasome activity. Instead, NLRP3 induction led to the differentiation of pink1 KO BAPs into white-like adipocytes by increasing the expression of white adipocyte-specific genes and repressing the expression of brown adipocyte-specific genes. nlrp3 deletion in pink1 knockout mice reversed BAT dysfunction. Conversely, adipose tissue-specific atg7 KO mice showed significantly lower expression of Nlrp3 in their BAT. Overall, our data suggest that the role of mitophagy is different from general autophagy in regulating adipose tissue and whole-body energy metabolism. Our results uncovered a new mitochondria-NLRP3 pathway that induces BAT dysfunction. The ability of the nlrp3 knockouts to rescue BAT dysfunction suggests the transcriptional function of NLRP3 as an unexpected, but a quite specific therapeutic target for obesity-related metabolic diseases.Abbreviations: ACTB: actin, beta; BAPs: brown adipocyte precursors; BAT: brown adipose tissue; BMDMs: bone marrow-derived macrophages; CASP1: caspase 1; CEBPA: CCAAT/enhancer binding protein (C/EBP), alpha; ChIP: chromatin immunoprecipitation; EE: energy expenditure; HFD: high-fat diet; IL1B: interleukin 1 beta; ITT: insulin tolerance test; KO: knockout; LPS: lipopolysaccharide; NLRP3: NLR family, pyrin domain containing 3; PINK1: PTEN induced putative kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RD: regular diet; ROS: reactive oxygen species; RT: room temperature; UCP1: uncoupling protein 1 (mitochondrial, proton carrier); WT: wild-type.
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Affiliation(s)
- Myoung Seok Ko
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ji Young Yun
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - In-Jeoung Baek
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Eun Jang
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Jin Hwang
- Institute for Innovative Cancer Research, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seung Eun Lee
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seung-Ho Heo
- Convergence Medicine Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - David A. Bader
- Molecular and Cellular Biology and Medicine, Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, Texas, USA
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jaeseok Han
- Soonchunhyang Institute of Med-bio Science (SIMS), Soonchunhyang University, Korea
| | - Jong-Seok Moon
- Soonchunhyang Institute of Med-bio Science (SIMS), Soonchunhyang University, Korea
| | - Jae Man Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Eun-Gyoung Hong
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Korea
| | - In-Kyu Lee
- Department of Internal Medicine and Biochemistry, Kyungpook National University School of Medicine, Daegu, Korea
| | - Seong Who Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Joong Yeol Park
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sean M. Hartig
- Molecular and Cellular Biology and Medicine, Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, Texas, USA
| | - Un Jung Kang
- Department of Neurology, Neuroscience and Physiology, Marlene and Paolo Fresco Institute for Parkinson’s and Movement Disorders, NYU Langone Health, New York, USA
| | - David D. Moore
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Eun Hee Koh
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ki-up Lee
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Nakajima W, Miyazaki K, Asano Y, Kubota S, Tanaka N. Krüppel-Like Factor 4 and Its Activator APTO-253 Induce NOXA-Mediated, p53-Independent Apoptosis in Triple-Negative Breast Cancer Cells. Genes (Basel) 2021; 12:genes12040539. [PMID: 33918002 PMCID: PMC8068402 DOI: 10.3390/genes12040539] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/19/2023] Open
Abstract
Inducing apoptosis is an effective treatment for cancer. Conventional cytotoxic anticancer agents induce apoptosis primarily through activation of tumor suppressor p53 by causing DNA damage and the resulting regulation of B-cell leukemia/lymphoma-2 (BCL-2) family proteins. Therefore, the effects of these agents are limited in cancers where p53 loss-of-function mutations are common, such as triple-negative breast cancer (TNBC). Here, we demonstrate that ultraviolet (UV) light-induced p53-independent transcriptional activation of NOXA, a proapoptotic factor in the BCL-2 family, results in apoptosis induction. This UV light-induced NOXA expression was triggered by extracellular signal-regulated kinase (ERK) activity. Moreover, we identified the specific UV light-inducible DNA element of the NOXA promoter and found that this sequence is responsible for transcription factor Krüppel-like factor 4 (KLF4)-mediated induction. In p53-mutated TNBC cells, inhibition of KLF4 by RNA interference reduced NOXA expression. Furthermore, treatment of TNBC cells with a KLF4-inducing small compound, APTO-253, resulted in the induction of NOXA expression and NOXA-mediated apoptosis. Therefore, our results help to clarify the molecular mechanism of DNA damage-induced apoptosis and provide support for a possible treatment method for p53-mutated cancers.
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Ngo KA, Kishimoto K, Davis-Turak J, Pimplaskar A, Cheng Z, Spreafico R, Chen EY, Tam A, Ghosh G, Mitchell S, Hoffmann A. Dissecting the Regulatory Strategies of NF-κB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation Logics. Cell Rep 2021; 30:2758-2775.e6. [PMID: 32101750 PMCID: PMC7061728 DOI: 10.1016/j.celrep.2020.01.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/23/2019] [Accepted: 01/30/2020] [Indexed: 01/22/2023] Open
Abstract
Nuclear factor κB (NF-κB) RelA is the potent transcriptional activator of inflammatory response genes. We stringently defined a list of direct RelA target genes by integrating physical (chromatin immunoprecipitation sequencing [ChIP-seq]) and functional (RNA sequencing [RNA-seq] in knockouts) datasets. We then dissected each gene’s regulatory strategy by testing RelA variants in a primary-cell genetic-complementation assay. All endogenous target genes require RelA to make DNA-base-specific contacts, and none are activatable by the DNA binding domain alone. However, endogenous target genes differ widely in how they employ the two transactivation domains. Through model-aided analysis of the dynamic time-course data, we reveal the gene-specific synergy and redundancy of TA1 and TA2. Given that post-translational modifications control TA1 activity and intrinsic affinity for coactivators determines TA2 activity, the differential TA logics suggests context-dependent versus context-independent control of endogenous RelA-target genes. Although some inflammatory initiators appear to require co-stimulatory TA1 activation, inflammatory resolvers are a part of the NF-κB RelA core response. Ngo et al. developed a genetic complementation system for NF-κB RelA that reveals that NF-κB target-gene selection requires high-affinity RelA binding and transcriptional activation domains for gene induction. The synergistic and redundant functions of two transactivation domains define pro-inflammatory and inflammation-response genes.
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Affiliation(s)
- Kim A Ngo
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kensei Kishimoto
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jeremy Davis-Turak
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aditya Pimplaskar
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhang Cheng
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Roberto Spreafico
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emily Y Chen
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amy Tam
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92037, USA
| | - Simon Mitchell
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Liu N, Guan H, Niu G, Jiang L, Li Y, Zhang J, Li J, Tan H. Molecular mechanism of mureidomycin biosynthesis activated by introduction of an exogenous regulatory gene ssaA into Streptomyces roseosporus. Sci China Life Sci 2021; 64:1949-63. [PMID: 33580428 DOI: 10.1007/s11427-020-1892-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/26/2021] [Indexed: 12/04/2022]
Abstract
Mureidomycins (MRDs), a group of unique uridyl-peptide antibiotics, exhibit antibacterial activity against the highly refractory pathogen Pseudomonas aeruginosa. Our previous study showed that the cryptic MRD biosynthetic gene cluster (BGC) mrd in Streptomyces roseosporus NRRL 15998 could not be activated by its endogenous regulator 02995 but activated by an exogenous activator SsaA from sansanmycin’s BGC ssa of Streptomyces sp. strain SS. Here we report the molecular mechanism for this inexplicable regulation. EMSAs and footprinting experiments revealed that SsaA could directly bind to a 14-nt palindrome sequence of 5′-CTGRCNNNNGTCAG-3′ within six promoter regions of mrd. Disruption of three representative target genes (SSGG-02981, SSGG-02987 and SSGG-02994) showed that the target genes directly controlled by SsaA were essential for MRD production. The regulatory function was further investigated by replacing six regions of SSGG-02995 with those of ssaA. Surprisingly, only the replacement of 343–450 nt fragment encoding the 115–150 amino acids (AA) of SsaA could activate MRD biosynthesis. Further bioinformatics analysis showed that the 115–150 AA situated between two conserved domains of SsaA. Our findings significantly demonstrate that constitutive expression of a homologous exogenous regulatory gene is an effective strategy to awaken cryptic biosynthetic pathways in Streptomyces.
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Xu N, Meng L, Song L, Li X, Du S, Hu F, Lv Y, Song W. Identification and Characterization of Secondary Wall-Associated NAC Genes and Their Involvement in Hormonal Responses in Tobacco ( Nicotiana tabacum). Front Plant Sci 2021; 12:712254. [PMID: 34594349 PMCID: PMC8476963 DOI: 10.3389/fpls.2021.712254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/12/2021] [Indexed: 05/02/2023]
Abstract
Secondary wall-associated NAC (SWN) genes are a subgroup of NAC (NAM, ATAF, and CUC) transcription factors (TF) that play a key role in regulating secondary cell wall biosynthesis in plants. However, this gene family has not been systematically characterized, and their potential roles in response to hormones are unknown in Nicotiana tabacum. In this study, a total of 40 SWN genes, of which 12 from Nicotiana tomentosiformis, 13 from Nicotiana sylvestris, and 15 from Nicotiana tabacum, were successfully identified. The 15 SWNs from Nicotiana tabacum were further classified into three groups, namely, vascular-related NAC domain genes (NtVNDs), NAC secondary wall thickening promoting factor genes (NtNSTs), and secondary wall-associated NAC domain genes (NtSNDs). The protein characteristic, gene structure, and chromosomal location of 15 NtSWNs (also named Nt1 to Nt15) were also analyzed. The NtVND and NtNST group genes had five conserved subdomains in their N-terminal regions and a motif (LP[Q/x] L[E/x] S[P/A]) in their diverged C- terminal regions. Some hormones, dark and low-temperature related cis-acting elements, were significantly enriched in the promoters of NtSWN genes. A comprehensive expression profile analysis revealed that Nt4 and Nt12 might play a role in vein development. Others might be important for stem development. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) revealed that in the NtNST group, genes such as Nt7, Nt8, and Nt13 were more sensitive than the genes in NtVND and NtSND groups under abiotic stress conditions. A transactivation assay further suggested that Nt7, Nt8, and Nt13 showed a significant transactivation activity. Overall, SWN genes were finally identified and characterized in diploid and tetraploid tobacco, revealing new insights into their evolution, variation, and homology relationships. Transcriptome, cis-acting element, qRT-PCR, and transactivation assay analysis indicated the roles in hormonal and stress responses, which provided further resources in molecular mechanism and genetic improvement.
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Affiliation(s)
- Na Xu
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lin Meng
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lin Song
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xiaoxu Li
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Shasha Du
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Yuanda Lv
| | - Wenjing Song
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Wenjing Song
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Stec N, Doerfel K, Hills-Muckey K, Ettorre VM, Ercan S, Keil W, Hammell CM. An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output during C. elegans Development. Curr Biol 2021; 31:809-826.e6. [PMID: 33357451 DOI: 10.1016/j.cub.2020.11.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022]
Abstract
Although precise tuning of gene expression levels is critical for most developmental pathways, the mechanisms by which the transcriptional output of dosage-sensitive molecules is established or modulated by the environment remain poorly understood. Here, we provide a mechanistic framework for how the conserved transcription factor BLMP-1/Blimp1 operates as a pioneer factor to decompact chromatin near its target loci during embryogenesis (hours prior to major transcriptional activation) and, by doing so, regulates both the duration and amplitude of subsequent target gene transcription during post-embryonic development. This priming mechanism is genetically separable from the mechanisms that establish the timing of transcriptional induction and functions to canalize aspects of cell-fate specification, animal size regulation, and molting. A key feature of the BLMP-1-dependent transcriptional priming mechanism is that chromatin decompaction is initially established during embryogenesis and maintained throughout larval development by nutrient sensing. This anticipatory mechanism integrates transcriptional output with environmental conditions and is essential for resuming normal temporal patterning after animals exit nutrient-mediated developmental arrests.
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Riber L, Løbner‐Olesen A. Inhibition of Escherichia coli chromosome replication by rifampicin treatment or during the stringent response is overcome by de novo DnaA protein synthesis. Mol Microbiol 2020; 114:906-919. [PMID: 32458540 PMCID: PMC7818497 DOI: 10.1111/mmi.14531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 12/15/2022]
Abstract
Initiation of Escherichia coli chromosome replication is controlled by the DnaA initiator protein. Both rifampicin-mediated inhibition of transcription and ppGpp-induced changes in global transcription stops replication at the level of initiation. Here, we show that continued DnaA protein synthesis allows for replication initiation both during the rifampicin treatment and during the stringent response when the ppGpp level is high. A reduction in or cessation of de novo DnaA synthesis, therefore, causes the initiation arrest in both cases. In accordance with this, inhibition of translation with chloramphenicol also stops initiations. The initiation arrest caused by rifampicin was faster than that caused by chloramphenicol, despite of the latter inhibiting DnaA accumulation immediately. During chloramphenicol treatment transcription is still ongoing and we suggest that transcriptional events in or near the origin, that is, transcriptional activation, can allow for a few extra initiations when DnaA becomes limiting. We suggest, for both rifampicin treated cells and for cells accumulating ppGpp, that a turn-off of initiation from oriC requires a stop in de novo DnaA synthesis and that an additional lack of transcriptional activation enhances this process, that is, leads to a faster initiation stop.
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Affiliation(s)
- Leise Riber
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
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Sui YB, Zhang KK, Ren YK, Liu L, Liu Y. The role of Nrf2 in astragaloside IV-mediated antioxidative protection on heart failure. Pharm Biol 2020; 58:1192-1198. [PMID: 33253607 PMCID: PMC7717863 DOI: 10.1080/13880209.2020.1849319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/28/2020] [Accepted: 11/04/2020] [Indexed: 05/27/2023]
Abstract
CONTEXT Heart failure is one of the most serious diseases worldwide. Astragaloside IV (ASI) is widely used in the treatment of cardiovascular diseases. OBJECTIVE To elucidate the antioxidative mechanism of ASI in a rat model of left coronary artery ligation. MATERIALS AND METHODS Left coronary artery of Sprague-Dawley rats was ligated to establish the model of heart failure, and then vehicle (saline) or ASI (1 mg/kg/day) was orally administered to the rats (n = 15) for 6 weeks. Echocardiography was used to evaluate the cardiac function. Myocardial infarct size was measured by triphenyltetrazolium chloride staining. Oxidative stress in the ventricular myocardium was determined. Molecular mechanisms were investigated by Western blot and chromatin immunoprecipitation. RESULTS ASI improved the cardiac function, especially ejection fraction (75.27 ± 5.75% vs. 36.26 ± 4.14%) and fractional shortening (45.39 ± 3.66% vs. 17.88 ± 1.32%), and reduced the infarct size of left ventricle (20.69 ± 2.98% vs. 39.11 ± 3.97%). ASI maintained the levels of glutathione, catalase and superoxide dismutase and prevented the leakage of creatine kinase. In addition, ASI induced the protein expression of Nrf2 (1.97-fold) and HO-1 (2.79-fold), while reduced that of Keap-1 (0.77-fold) in the ventricular myocardium. In H9c2 cells, a rat cardiomyocyte cell line, ASI induced the translocation of Nrf2 from cytoplasm to nucleus, followed by transcriptional activation of NQO-1 (8.27-fold), SOD-2 (3.27-fold) and Txn-1 (9.83-fold) genes. DISCUSSION AND CONCLUSIONS ASI prevented heart failure by counteracting oxidative stress through the Nrf2/HO-1 pathway. Application in clinical practice warrants further investigation.
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Affiliation(s)
- Yan-Bo Sui
- Department of Cardiology, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Kui-Kui Zhang
- Department of Cardiology, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yu-kun Ren
- Department of Dermatology, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Li Liu
- Department of Cardiology, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yan Liu
- Department of Scientific Research Management, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
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Pascual-Ahuir A, Fita-Torró J, Proft M. Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:E8278. [PMID: 33167354 DOI: 10.3390/ijms21218278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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Sun Y, Gao J, Jing Z, Zhao Y, Sun Y, Zhao X. PURα Promotes the Transcriptional Activation of PCK2 in Oesophageal Squamous Cell Carcinoma Cells. Genes (Basel) 2020; 11:genes11111301. [PMID: 33142842 PMCID: PMC7692967 DOI: 10.3390/genes11111301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/15/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal gastrointestinal malignancies due to its characteristics of local invasion and distant metastasis. Purine element binding protein α (PURα) is a DNA and RNA binding protein, and recent studies have showed that abnormal expression of PURα is associated with the progression of some tumors, but its oncogenic function, especially in ESCC progression, has not been determined. Based on the bioinformatic analysis of RNA-seq and ChIP-seq data, we found that PURα affected metabolic pathways, including oxidative phosphorylation and fatty acid metabolism, and we observed that it has binding peaks in the promoter of mitochondrial phosphoenolpyruvate carboxykinase (PCK2). Meanwhile, PURα significantly increased the activity of the PCK2 gene promoter by binding to the GGGAGGCGGA motif, as determined though luciferase assay and ChIP-PCR/qPCR. The results of Western blotting and qRT-PCR analysis showed that PURα overexpression enhances the protein and mRNA levels of PCK2 in KYSE510 cells, whereas PURα knockdown inhibits the protein and mRNA levels of PCK2 in KYSE170 cells. In addition, measurements of the oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) indicated that PURα promoted the metabolism of ESCC cells. Taken together, our results help to elucidate the molecular mechanism by which PURα activates the transcription and expression of PCK2, which contributes to the development of a new therapeutic target for ESCC.
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